GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Klebsiella michiganensis M5al

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate BWI76_RS27020 BWI76_RS27020 xylulokinase

Query= reanno::Koxy:BWI76_RS27020
         (484 letters)



>FitnessBrowser__Koxy:BWI76_RS27020
          Length = 484

 Score =  981 bits (2537), Expect = 0.0
 Identities = 484/484 (100%), Positives = 484/484 (100%)

Query: 1   MYIGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALG 60
           MYIGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALG
Sbjct: 1   MYIGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALG 60

Query: 61  AQHSLRAVKALGIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVSRSRQITG 120
           AQHSLRAVKALGIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVSRSRQITG
Sbjct: 61  AQHSLRAVKALGIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVSRSRQITG 120

Query: 121 NLMMPGFTAPKLLWVQRHEPEIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDVA 180
           NLMMPGFTAPKLLWVQRHEPEIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDVA
Sbjct: 121 NLMMPGFTAPKLLWVQRHEPEIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDVA 180

Query: 181 RRDWSDEMLAACGLSRDNMPALFEGCEVTGSLRPAVAQAWNMPEVLVVAGGGDNAAGAVG 240
           RRDWSDEMLAACGLSRDNMPALFEGCEVTGSLRPAVAQAWNMPEVLVVAGGGDNAAGAVG
Sbjct: 181 RRDWSDEMLAACGLSRDNMPALFEGCEVTGSLRPAVAQAWNMPEVLVVAGGGDNAAGAVG 240

Query: 241 VGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHALPGRWHLMSVMLSAASCLDW 300
           VGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHALPGRWHLMSVMLSAASCLDW
Sbjct: 241 VGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHALPGRWHLMSVMLSAASCLDW 300

Query: 301 AATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPAE 360
           AATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPAE
Sbjct: 301 AATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPAE 360

Query: 361 LARAVLEGVGYALADGMDVVHACGVKPESVTLIGGGARSAYWRQMLADISGQQLDFRTGG 420
           LARAVLEGVGYALADGMDVVHACGVKPESVTLIGGGARSAYWRQMLADISGQQLDFRTGG
Sbjct: 361 LARAVLEGVGYALADGMDVVHACGVKPESVTLIGGGARSAYWRQMLADISGQQLDFRTGG 420

Query: 421 DVGPALGAARLAQLALHRNVAFSDLLPQLPLEQAHLPDAERFARYAPRRETFRQIYQQLL 480
           DVGPALGAARLAQLALHRNVAFSDLLPQLPLEQAHLPDAERFARYAPRRETFRQIYQQLL
Sbjct: 421 DVGPALGAARLAQLALHRNVAFSDLLPQLPLEQAHLPDAERFARYAPRRETFRQIYQQLL 480

Query: 481 PLMS 484
           PLMS
Sbjct: 481 PLMS 484


Lambda     K      H
   0.320    0.134    0.417 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 944
Number of extensions: 32
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 484
Length of database: 484
Length adjustment: 34
Effective length of query: 450
Effective length of database: 450
Effective search space:   202500
Effective search space used:   202500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate BWI76_RS27020 BWI76_RS27020 (xylulokinase)
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01312.hmm
# target sequence database:        /tmp/gapView.31220.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01312  [M=481]
Accession:   TIGR01312
Description: XylB: xylulokinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.2e-191  621.0   0.0   7.1e-191  620.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS27020  BWI76_RS27020 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS27020  BWI76_RS27020 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  620.8   0.0  7.1e-191  7.1e-191       1     481 []       3     477 ..       3     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 620.8 bits;  conditional E-value: 7.1e-191
                               TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikai 71 
                                             +GiDlgTs+vKa+l++e+gev+as++++l+v++p+p wsEqdpe+w+ a+++a+k+l ++++   +++ka+
  lcl|FitnessBrowser__Koxy:BWI76_RS27020   3 IGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALGAQHS--LRAVKAL 71 
                                             8***********************************************************88..59***** PP

                               TIGR01312  72 sisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhep 142
                                             +i+GQmHg++lLD++++vlrpaiLWnD r+ eec+ lee++   +++++tgnl+++gfTapKllWv++hep
  lcl|FitnessBrowser__Koxy:BWI76_RS27020  72 GIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVS--RSRQITGNLMMPGFTAPKLLWVQRHEP 140
                                             *****************************************7..9************************** PP

                               TIGR01312 143 evfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGk 213
                                             e+f++++kvlLPkDylr+++tge+++++sDA+GT++ dv++r+ws+e+l+a+ l+++ +P+l+e++e++G+
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 141 EIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDVARRDWSDEMLAACGLSRDNMPALFEGCEVTGS 211
                                             *********************************************************************** PP

                               TIGR01312 214 vreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchal 284
                                             +r++va+++ +  +v v+aGggdnaagA+G+g+ ++g++++slGtSGv++av+d   s+pe+avhsFchal
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 212 LRPAVAQAWNM-PEVLVVAGGGDNAAGAVGVGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHAL 281
                                             *********99.78********************************************************* PP

                               TIGR01312 285 pgkwyplgvtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGl 355
                                             pg+w+ ++v+lsa+s+l+w++ l+g  +v +l ++ae+++ +a++v++lPylsGERtPh++pqa+g+++Gl
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 282 PGRWHLMSVMLSAASCLDWAATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKGVFFGL 352
                                             *********************************************************************** PP

                               TIGR01312 356 tanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eee 425
                                             t+++  a+larAvlegv +al+d++d++++ +g+k+++++liGGGa+s++wrq+ladi+g++++ ++  + 
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 353 THQHGPAELARAVLEGVGYALADGMDVVHA-CGVKPESVTLIGGGARSAYWRQMLADISGQQLDFRTgGDV 422
                                             *****************************9.88**********************************99** PP

                               TIGR01312 426 gaalGaAilAaialg.ekdlveecseavvkqkesvepiaenveayeelyerykklye 481
                                             g+alGaA+lA++al+ + +  +++++   +q +   p+ae+ ++y+ + e+++++y+
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 423 GPALGAARLAQLALHrNVAFSDLLPQLPLEQAHL--PDAERFARYAPRRETFRQIYQ 477
                                             **************96666677788888887777..******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (484 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 6.80
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory